{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T00:54:50Z","timestamp":1775523290145,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,12,28]],"date-time":"2021-12-28T00:00:00Z","timestamp":1640649600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007316","name":"Klaus Tschira Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007316","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The assessment of novel phylogenetic models and inference methods is routinely being conducted via experiments on simulated as well as empirical data. When generating synthetic data it is often unclear how to set simulation parameters for the models and generate trees that appropriately reflect empirical model parameter distributions and tree shapes. As a solution, we present and make available a new database called \u2018RAxML Grove\u2019 currently comprising more than 60\u00a0000 inferred trees and respective model parameter estimates from fully anonymized empirical datasets that were analyzed using RAxML and RAxML-NG on two web servers. We also describe and make available two simple applications of RAxML Grove to exemplify its usage and highlight its utility for designing realistic simulation studies and analyzing empirical model parameter and tree shape distributions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>RAxML Grove is freely available at https:\/\/github.com\/angtft\/RAxMLGrove.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab863","type":"journal-article","created":{"date-parts":[[2021,12,22]],"date-time":"2021-12-22T07:52:16Z","timestamp":1640159536000},"page":"1741-1742","source":"Crossref","is-referenced-by-count":24,"title":["RAxML Grove: an empirical phylogenetic tree database"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4144-6709","authenticated-orcid":false,"given":"Dimitri","family":"H\u00f6hler","sequence":"first","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , 69118 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wayne","family":"Pfeiffer","sequence":"additional","affiliation":[{"name":"San Diego Supercomputer Center, University of California, San Diego , La Jolla, CA 92093-0505, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vassilios","family":"Ioannidis","sequence":"additional","affiliation":[{"name":"Core-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heinz","family":"Stockinger","sequence":"additional","affiliation":[{"name":"Core-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0353-0691","authenticated-orcid":false,"given":"Alexandros","family":"Stamatakis","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , 69118 Heidelberg, Germany"},{"name":"Institute for Theoretical Informatics, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,12,28]]},"reference":[{"key":"2023020108581744600_btab863-B1","doi-asserted-by":"crossref","first-page":"iii31","DOI":"10.1093\/bioinformatics\/bti1200","article-title":"DNA assembly with gaps (Dawg): simulating sequence evolution","volume":"21","author":"Cartwright","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020108581744600_btab863-B2","doi-asserted-by":"crossref","first-page":"1286","DOI":"10.1093\/bioinformatics\/btz710","article-title":"Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages","volume":"36","author":"Dav\u00edn","year":"2020","journal-title":"Bioinformatics"},{"key":"2023020108581744600_btab863-B3","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"Drummond","year":"2012","journal-title":"Mol. 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